Concurrent mapping of brain ontogeny and phylogeny within a common space: Standardized tractography and applications

Developmental and evolutionary effects on brain organization are complex, yet linked, as evidenced by the correspondence in cortical area expansion across these vastly different time scales. However, it is still not possible to study concurrently the ontogeny and phylogeny of cortical areal connections, which is arguably more relevant to brain function than allometric measurements. Here, we propose a novel framework that allows the integration of structural connectivity maps from humans (adults and neonates) and nonhuman primates (macaques) onto a common space. We use white matter bundles to anchor the common space and use the uniqueness of cortical connection patterns to these bundles to probe area specialization. This enabled us to quantitatively study divergences and similarities in connectivity over evolutionary and developmental scales, to reveal brain maturation trajectories, including the effect of premature birth, and to translate cortical atlases between diverse brains. Our findings open new avenues for an integrative approach to imaging neuroanatomy.


Superior Longitudinal Fasciculus (SLF) 1/2/3
The superior longitudinal fasciculus is a longitudinal parieto-frontal tract associated with visuospatial attention (56). It can be separated into three bundles: a dorsal superior longitudinal fasciculus SLF1, middle SLF2 and ventral SLF3. For each bundle, a coronal plane in the region of the central sulcus within the frontoparietal cortex is used as a seed, along with two target masks. The frontal target masks for the first, second and third branches of the SLF were coronal sections through the superior, middle and inferior frontal gyri, respectively, placed at the level of the posterior end of the corpus callosum. Posteriorly, a large coronal target mask in the superior parietal lobule, immediately posterior to the margin of the cingulate gyrus is used for SLF1. For SLF2 and SLF3, the second target masks are placed in the angular gyrus and supramarginal gyrus respectively. In each case, seed placement reflects the placement of the second target whilst being moved anteriorly into the region of the central sulcus. For each protocol, an axial exclusion mask was placed underneath the parietal cortex, and one blocking subcortical areas prevented leakage into ventrally oriented fibres. A coronal exclusion mask through subcortical areas posterior to the caudal end of the genu of the corpus callosum prevented streamlines leaking into ventral longitudinal tracts. The SLFs are still maturing during the neonatal period, which makes them challenging to delineate in this age-group (86). Therefore, extra exclusion masks were added compared to the adult protocols, to help constrain the tractography. For each branch, the target masks for each of the other SLF branches were included as exclusion masks. An additional exclusion mask was also placed in the cingulate gyrus for the SLF1, to prevent leakage into this region. The seed and target masks were also increased in size relative to the anatomy, compared to the adult masks, which made the results more robust.

Uncinate Fasciculus (UF)
The uncinate fasciculus is a hook-shaped bundle that connects the frontal lobe with the anterior temporal lobe. The tract was reconstructed using a seed in the STG at the first location where the temporal and frontal cortex are separated, and a target through the ventral part of the extreme capsule. An exclusion mask layer was added between the seed and the target to force the streamlines to curve between them. A coronal exclusion mask prevented leakage into the fibres running longitudinally through the temporal lobe. For the neonatal protocols, an additional axial exclusion mask was added to prevent fibres leaking into the external capsule.

Vertical Occipital Fasciculus (VOF)
The vertical occipital fasciculus runs in a predominantly dorsal-ventral orientation in the occipital lobe. The original protocol was adapted from ref. (87). An axial seed mask was placed in the lateral part of the ventral occipital white matter posterior to the anterior occipital sulcus. A larger anterior target mask was placed dorsally at the level of the lateral occipital sulcus. A coronal plane just posterior to the corpus callosum served as an exclusion mask, to prevent leakage into anteriorposterior tracts.

Commissural Fibres
Anterior Commissure (AC) The anterior commissure connects the temporal lobes of the two hemispheres across the midline. It was seeded in the left-right oriented fibres on the midline, with a target mask covering the white matter lateral to the globus pallidae. Stop masks were placed directly underneath and lateral to the two amygdalae. A large axial exclusion mask was placed dorsal to the seed through the entire subcortex. For the neonatal protocols, an axial exclusion mask was added covering the optic chiasm to prevent leakage into the optic nerve. A further coronal axial exclusion mask was added in the anterior limb of the internal capsule, to prevent erroneous frontal projections from the seed.

Corpus Callosum, Splenium (FMA) and Genu (FMI)
Callosal connections to the occipital lobe were constructed via the splenium of the corpus callosum (forceps major, FMA) and to the frontal lobe via the genu of the corpus callosum (forceps minor, FMI), using recipes based on those defined by ref. (88). Seed and target masks, and their inverse, for the FMA were defined as coronal sections through the occipital lobe at the posterior end of the parietal occipital sulcus. The sagittal exclusion mask was confined to the occipital cortex and the subcortex. Additional exclusion masks through the inferior fronto-occipital white matter and a coronal plane through the pons prevented leakage into the longitudinal fibres. Seed and target masks (and their inverse) for the FMI were defined as coronal sections through the frontal lobe at the anterior end of the pregenual cingulate sulcus. The midsagittal exclusion mask was interrupted at the level of the anterior third of the corpus callosum, and an additional coronal exclusion mask at the same level prevents posterior projections.

Middle Cerebella Peduncle (MCP)
The middle cerebellar peduncle connects the cerebellum to the pons. This tract was seeded in the cerebellar white matter with a target in the opposite hemisphere (and their inverses). Exclusion masks were placed sagittally along the cerebellar midline and axially through the thalamus.

Limbic Fibres Cingulum Subsections (CBT, CBP, CBD)
The cingulum facilitates communication between different parts of the limbic system. It projects from the cingulate gyrus to the entorhinal cortex (89). Protocols were defined for three distinct sections of the cingulum, based on a recent segmentation by ref. (88). The temporal part (CBT) was seeded in the posterior part of the temporal lobe at a section where the fibres of the cingulum are mostly oriented in the anterior-posterior direction. The target was placed posteriorly to the amygdala. Stop masks were placed posteriorly and anteriorly to the seed and target masks, respectively. An exclusion mask prevented leakage into the fornix. The dorsal segment (CBD) was seeded just above the posterior part of the corpus callosum and had a target at the start of the genu of the corpus callosum. A sagittal exclusion mask in the anterior limb of the internal capsule prevented leakage into the temporal lobe. Finally, the peri-genual part of the cingulum bundle (CBP) was seeded anteriorly above the corpus callosum and a target placed below the sub-genual callosum with a stop mask placed inferior and anterior to the target. A callosal plane at the level of the rostral end of the Sylvian fissure prevented leakage into the CBD.

Fornix (FX)
The fornix connects the hippocampus with the mammillary bodies, the anterior thalamic nuclei, and the hypothalamus (91). The tract was reconstructed using a seed in the body of the fornix at the level of the middle of the corpus callosum and a target in the hippocampus. A callosal plane at the anterior end of the occipital cortex prevented leakage into posterior tracts. To prevent leakage into the cingulum, an axial exclusion mask posterior to the splenium of the corpus callosum, and a small axial exclusion covering the parahippocampal gyrus region of the cingulum are also used. The adult protocol contains bilateral sagittal planes around the midline, at the level of the anterior tip of the thalamus, to prevent lateral propagation to the anterior limb of the internal capsule. These exclusion masks were reduced in size for the neonatal protocol, relative to the adult protocol, as they were found to hinder fibre tracking in the neonates.

Projection Fibres Acoustic Radiation (AR)
The acoustic radiation connects the medial geniculate nucleus (MGN) of the thalamus to the auditory cortex. It was seeded from the transverse temporal gyrus with a target covering the MGN of the thalamus. The exclusion mask consists of two coronal planes, anterior and posterior to the thalamus, as well as a mask covering the brainstem and a horizontal region covering the optic tract. The adult protocol contains an axial plane superior to the thalamus as an exclusion mask. This mask was moved inferiorly for the neonatal protocols, to stop leakage into the internal capsule.

Anterior Thalamic Radiation (ATR)
The anterior thalamic radiation connects the thalamus to the frontal lobe. It is seeded using a coronal mask through the anterior part of the thalamus (88), with a coronal target mask at the anterior thalamic peduncle. In addition, the exclusion mask contains an axial plane covering the base of the midbrain, a coronal plane preventing leakage via the posterior thalamic peduncle and a coronal plane preventing leakage via the cingulum. A coronal stop mask covers the posterior part of the thalamus, extending from the base of the midbrain to the callosal sulcus. An additional axial exclusion mask was added compared to the adult protocol at the level of the cingulate gyrus, to prevent contamination from fibres in the superior thalamic radiation.

Corticospinal tract (CST)
The corticospinal, or pyramidal, tract extends from the spinal cord through the midbrain and distributes to motor cortex, premotor cortex and somatosensory cortex. The tracts is seeded from the pons with a large target covering the motor, premotor and somatosensory cortices. An axial exclusion mask us used to restrict tracking to the cerebral peduncle of the midbrain. In addition, the exclusion mask includes two coronal planes, anterior and posterior to the target, to exclude tracking to the prefrontal cortex and occipital cortex respectively, and a plane preventing leakage into the cerebellar peduncles. To prevent contamination from the spino-thalamic tract, an additional exclusion mask was added in the neonatal protocol, in the posterior part of the brainstem.

Optic Radiation (OR)
The optic radiation consists of fibres connecting the lateral geniculate nucleus (LGN) of the thalamus to the primary visual cortex. It was seeded in the LGN, with a target mask through the anterior part of the calcarine fissure. Exclusion masks consisted of an axial block in the brainstem, a coronal plane directly posterior to the LGN to select fibres that curl around dorsally, and a coronal plane anterior to the seed to prevent leakage into longitudinal fibres. In addition, a further axial exclusion mask was added in the neonatal protocols, anterior to the target mask, to restrict fibres travelling to the parietal lobe.

Superior Thalamic Radiation (STR)
The superior thalamic radiation connects the thalamus to the pre-/post-central gyrus. It was seeded using a mask covering the whole thalamus and an axial target plane covering the superior thalamic peduncle. An axial plane is used as a stop mask ventrally to the thalamus. The exclusion mask includes two coronal planes anterior and posterior to the target, to exclude tracking to the prefrontal cortex and occipital cortex, respectively.

Fig. S4. Association between phylogeny/ontogeny divergence and connectivity profile entropy.
Connectivity profile complexity was calculated at each cortical vertex = 1: , as the entropy of the profile ( = − ∑ log ∈ , X is the connectivity blueprint and T the set of tracts). The minimum KL divergence maps presented in Fig. 5(a-c) were compared to these entropy maps through brain-wide and local (i.e. spatially-moving windowed) correlation. The Fig. S6. Parcel-wise connectivity profiles across neonatal age groups and the adult brain. For visualisation, only the most highly contributing tracts are displayed (tract contribution > 0.05 to any group) and each plot area has been sum-normalised.  (Fig. 8b left). KL divergence matrices were calculated between group (neonate and adult) connectivity blueprints. Divergence matrices were then parcellated using the Brodmann cortical atlas for the adult brain and the Desikan-Killany cortical atlas for the neonatal brain, taking the median value for each region. We further define a set of anatomo-functional cortical systems (see Fig. 8). The inverse of the KL divergence matrices (i.e. the similarity) was then used as a feature set in spectral embedding and the first two components projected into a 2-dimensional space, colour-coded by major brain regions. Circles represent the Brodmann parcels for the adult brain and crosses represent the Desikan-Killany parcels for the neonate brain. Figure insets show the centre of gravity (median of parcel coordinates) for each anatomo-functionally defined cortical system for each brain. Legend key: "cing" = cingulate; "front" = frontal; "temp" = temporal; "trans" = transverse; "med" = medial; "mid" = "middle"; "inf" = inferior; "lat" = lateral; "ant" = anterior; "post" = posterior.  (Fig. 8b right). As above but now between the adult human and macaque brain, parcellated using the Brodmann cortical atlas. Circles represent the Brodmann parcels for the adult brain and crosses represent the Brodmann parcels for the macaque brain.   (37-40w, 40-42w, and 42-45w postmenstrual age (PMA)) used to assess protocol robustness across neonate age groups and to explore how divergence, with respect to the adult brain, changes with neonatal age -the number of subjects in each group is restricted to the minimum in any group. Bottom row: groups of premature and full-term neonates used to explore the effects of prematuritythe premature group is selected based on age at birth (<37w) and age at scan (37-45w) and full-term neonates are sub-selected from the full dHCP cohort to match for age at scan and sex.   Table S2. Acquisition details for the adult human and macaque data. Full acquisition details are available from the Human Connectome Project (HCP) (humanconnectome.org/hcp-protocols-ya-3t-imaging) and PRIME-DE database (fcon_1000.projects.nitrc.org/indi/PRIME/oxford2.html) for the human and macaque data respectively.